maxLikelihood: Growth rate estimate using Maximum Likelihood

In cloneRate: Estimate Growth Rates from Phylogenetic Trees

Growth rate estimate using Maximum Likelihood

Description

Uses the approximation that coalescence times H_i are equal to a+b*U_i to find a and b. b is equal to 1/r, where r is the net growth rate.

Usage

maxLikelihood(tree, alpha = 0.05)

Arguments

tree	An ultrametric tree subset to include only the clone of interest. Alternatively, a list with several such trees.
alpha	Used for calculation of confidence intervals. 1-alpha confidence intervals used with default of alpha = 0.05 (95 percent confidence intervals)

Value

A dataframe including the net growth rate estimate, confidence intervals, and other important details (clone age estimate, runtime, n, etc.)

See Also

internalLengths which uses an alternatvie method for growth rate estimation from an ultrametric tree.

Examples

df <- maxLikelihood(cloneRate::exampleUltraTrees[[1]])

cloneRate documentation built on Sept. 22, 2023, 5:09 p.m.